We have cloned and characterized a single-copy DNA sequence from the porcine α-1,3-galactosyltransferase gene that corresponds to a 547-base pair intron separating exons 3 and 4 of the protein coding domain. Polymerase chain reaction amplification of this sequence from flanking oligonucleotides generates a species-specific DNA probe (pgt34) capable of recognizing 50 pg chimeric template DNA at a pig to human cellular ratio of 1/10,000. Homologous DNA sequence is not identified in the macaque, baboon, or human genome by Southern hybridization. Analysis of a discordant model of pig to baboon xenotransplantation demonstrates peripheral blood microchimerism in the presence of a functioning pig kidney xenograft and persistence of microchimerism in lymphatic tissue after graft removal. This probe should be useful for tracking the fate of porcine cells in patients undergoing xenotransplantation of whole organs or free tissues such as pancreatic islet cells and should facilitate studies of microchimerism in experimental models of pig to monkey xenotransplantation.